Hypothesis of design of biological cell robot as human immunodeficiency virus vaccine

Table 1 Human immunodeficiency virus-related genes and their coding proteins, specific functions, and host-cell related proteins

Gene	Encoding protein	Protein function	Host cell-related proteins
Structural genes
gag	MA	Matrix proteins	Karyopherins, HO3, Calmodulin, VAN/NAF1, TRIM5α, CyPA
	CA	Capsid protein	HP68/RNase L inhibitor, Actin
	NC	Nucleocapsid protein	ESCRT, Tsg-101, AIP-1, Nedd4, Ubiquitin
	p6	Nucleocapsid protein	-
pol	RT	A viral genome that can be transcribed and copied	-
	PR	Cut polymerized protein	-
	IN	Integrate viral DNA with cellular DNA	INI1/hSNF5, LEDGF/p75, BAF, HMGal, ATR,
			ATM, Karyopherins, XRCC5
env	gp120	Attach the virus to the surface of the cell	CD4, CCR5. CXCR4, DC-SIGN, DC-SIGNR, MR, CD207
	gp41	Fusion with host cells	-
Necessary regulatory genes
tat	Tat	Trans-activated proteins that activate HIV gene transcription	NF-κB, cyclin T, CDK9, Med28
rev	Rev	A regulator of viral protein expression that regulates mRNA splicing and promotes mRNA transport to the cytoplasm	TNPO3, importin β, Crm1, Ran GTPase, Sam68, p32
Nonessential regulatory genes
nef	Nef	Negative regulatory factors, which change cell signals, reduce the expression of CD4 and MHC-I molecules, and reduce the killing of HIV infected cells by CTL, representing essential factors in the development of infection into AIDS	PACS-l, ASK1, PAK, PI3-K, Lck, VAN/NAFl
vif	Vif	Viral infectious factors that promote viral assembly and maturation	APOBEC3G
vpr	Vpr	Viral protein regulatory, which transports viral DMA to the nucleus and inhibits cell growth	Karyopherins, Uracil-DNA glycosylase, Weel
vpu	Vpu	Viral protein U that promotes the release of the virus	CD317 (Tetherin, BST-2)

HO3: Heme oxygenase-3; TRIM5α: TRIpartite motif-5α; CyPA: Cyclophilin A; ESCRT: Endosomal sorting complex required for transport; Tsg-101: Tumor susceptibility gene-101; AIP-1: Apoptosis-linked gene-2-interacting protein 1; Nedd4: Neural precursor cell expressed, developmentally down-regulated 4; INI1: Integrase interactor 1; BAF: Barrier-to-autointegration factor; ATR: Ataxia telangiectasia and RAD3-associated kinase; ATM: Ataxia telangiectasia-mutated gene; SIGN: Specific intercellular adhesion molecule-3-grabbing nonintergrin; DC-SIGNR: Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintergrin receptor; MR: Mannose receptor; HIV: Human immunodeficiency virus; NF-κB: Nuclear factor-κB; CDK9: Cyclin-dependent protein kinase 9; Med28: Mediator of RNA polymerase II transcription, subunit 28 homolog; TNPO3: Transportin-3; Crm1: Chromosome maintenance protein 1; Ran: Ras-related nuclear protein; Sam68: Src mitogen-associated protein 68 kDa; Nef: Negative regulate factor; CTL: Cytotoxic T lymphocytes; AIDS: Acquired immune deficiency syndrome; ASK1: Apoptotic signal-regulated kinase 1; PAK: p21 activated kinases; PI3-K: Phosphatidylinositol 3-kinases; Lck: Lymphocyte-specific protein-tyrosine kinase; VAN/NAF1: Virion associated nuclear shuttling protein/nef-associated factor 1; Vif: Viral infectivity factor; Vpr: Viral protein regulatory; Weel: Weel kinase is an important regulator to cell cycles; Vpu: Viral protein U.